title: Genome-wide transcriptome alternation by DNA methylation inhibitor 5'-Aza in primary leiomyoma cells

overall_design: Identify transcriptome changes between vehicle and 5'-Aza treated primary LM cells using RNA-Seq


title: Epigenomic Landscape of Mouse Brain by Single Nucleus Methylation Sequencing [CEMBA190219_9H]

status: Public on Oct 08 2020

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

type: Methylation profiling by high throughput sequencing

summary: Illustrating the cellular architecture of the mammalian brain is critical to understanding its diverse functions and complex animal behaviors. With support from NIMH and NINDS as part of the BRAIN Initiative Cell Census Network (BICCN), the Center for Epigenomics of the Mouse Brain Atlas (CEMBA) applied single nucleus methylation sequencing in 118 brain funtional regions across the whole adult male P56 C57BL/6J mouse brain. In each major brain regions, we identified distinct cell clusters and formed them in a hierarchical taxonomy. These clusters include known primary brain cell types and possible sub-types. We use these data to identify the epigenomic characteristics and to define specific regulatory elements for each cell cluster. We integrate the single cell methylome with single cell gene expression and chromatin accessibility profiles from the same brain region to further identify potential enhancers and their corresponding genes for several neuronal cell types. By brain region spacial comparisons, we found spatial specificity among excitatory neuronal clusters within the same cortical layer. We identify brain-region-specific transcription factors that may regulate cortical region development of excitatory neurons. These data define the landscape of cell type and spatial heterogeneity in the mouse brain and the underlining regulatory epigenomic basis.

overall_design: Apply snmC-seq2 to 118 brain functional regions to identify epigenomic landcape of the adult mouse brain, this subseries consists of one single nucleus methylation sequencing experiment of brain region (CA).

first: Hanqing

last: Liu

first: Chongyuan

last: Luo

first: Angeline

last: Rivkin

first: Anna

last: Bartlett

first: Jacinta

last: Lucero

last: Nery

first: Andrew

last: Aldridge

first: Rosa

last: Castanon

first: Yupeng

last: He

first: Huaming

last: Chen

first: Zhuzhu

last: Zhang

first: Jingtian

last: Zhou

first: Bing

last: Ren

first: Eran

middle: A

last: Mukamel

first: M

middle: M

last: Behrens


title: Epigenomic Landscape of Mouse Brain by Single Nucleus Methylation Sequencing [CEMBA190117_6A]

status: Public on Sep 29 2020

overall_design: Apply snmC-seq2 to 118 brain functional regions to identify epigenomic landcape of the adult mouse brain, this subseries consists of one single nucleus methylation sequencing experiment of brain region (ACA,PL,ILA).


title: Epigenomic Landscape of Mouse Brain by Single Nucleus Methylation Sequencing [CEMBA181220_5F]

status: Public on Sep 28 2020

overall_design: Apply snmC-seq2 to 118 brain functional regions to identify epigenomic landcape of the adult mouse brain, this subseries consists of one single nucleus methylation sequencing experiment of brain region (ACB).


title: Epigenomic Landscape of Mouse Brain by Single Nucleus Methylation Sequencing [CEMBA190122_6C]

overall_design: Apply snmC-seq2 to 118 brain functional regions to identify epigenomic landcape of the adult mouse brain, this subseries consists of one single nucleus methylation sequencing experiment of brain region (SSs).


title: Epigenomic Landscape of Mouse Brain by Single Nucleus Methylation Sequencing [CEMBA190212_9J]

status: Public on Oct 02 2020

overall_design: Apply snmC-seq2 to 118 brain functional regions to identify epigenomic landcape of the adult mouse brain, this subseries consists of one single nucleus methylation sequencing experiment of brain region (DG).


title: Epigenomic Landscape of Mouse Brain by Single Nucleus Methylation Sequencing [CEMBA190305_11F]

status: Public on Oct 10 2020


title: Epigenomic Landscape of Mouse Brain by Single Nucleus Methylation Sequencing [CEMBA190124_6C]

status: Public on Sep 30 2020


title: Targeting DNA Methylation Depletes Uterine Leiomyoma Stem Cell-enriched Population by Stimulating Their Differentiation

status: Public on Oct 01 2020

city: Chicago

first: Shimeng

state: Illinois

address: 320 East Superior Street

institute: Northwestern University

type: Expression profiling by high throughput sequencing

type: Genome binding/occupancy profiling by high throughput sequencing

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Callobius koreanus whole body and venom gland transcriptome

status: Public on Sep 26 2020

city: Goyang-si

first: Jungsuk

last: Sung

state: Gyeonggi-do

address: 32, Dongguk-ro, Ilsandong-gu

country: South Korea

institute: Life science

summary: Callobius koreanus (C.koreanus) is a wandering spider and a member of the Amaurobiidae family, infraorder Araneae. RNA-sequencing was performend for venom gland tissue and whole body except venom gland.

overall_design:
Callobius koreanus mRNA profiles of venom gland and whole body without venom gland

***Please note that the raw data files have been lost and thus are not included in the records.

first: Jung-Suk

first: Tae

middle: K

last: Seung

first: Hwang

last: In-Wook

first: Min Kyoung

last: Shin


title: Epigenomic Landscape of Mouse Brain by Single Nucleus Methylation Sequencing [CEMBA190207_5J]

first: Joseph

last: Ecker

overall_design: Apply snmC-seq2 to 118 brain functional regions to identify epigenomic landcape of the adult mouse brain, this subseries consists of one single nucleus methylation sequencing experiment of brain region (CP).

first: Hanqing

last: Liu

first: Chongyuan

last: Luo

first: Angeline

last: Rivkin

first: Anna


title: Comparative functional genome annotation of livestock species identifies core amniote regulatory features and avian enhancer versatility (H3K4me1 ChIP-Seq)

status: Public on Sep 24 2020

first: Colin

last: Kern

address: 9500 Gilman Dr

institute: UC San Diego

summary: Gene regulatory elements are central drivers of phenotypic variation and thus of critical importance towards understanding the genetics of complex traits. Here we present a genome-wide annotation of regulatory elements in a non-mammalian vertebrate, chicken (Gallus gallus), as well as two important agricultural mammalian species: pig (Sus scrofa) and cattle (Bos taurus), with chicken and pig in particular being important to human biology and medicine. This report is the first to employ all core assays as defined by the Functional Annotation of Animal Genomes (FAANG) consortium, including information from a wide range of epigenomic assays for the same eight diverse tissues of three livestock species. Comparative analysis of these datasets and those from the human and mouse ENCODE projects revealed that although less than half of enhancers are positionally conserved between species, a core set of regulatory elements are functionally conserved independent of evolutionary distance. Further analysis suggested that tissue-specific transcription factor occupancy at regulatory elements and their predicted target genes were also conserved. Interestingly, the smaller chicken genome – relative to mammals – contains a reduced number of enhancers; however, each chicken enhancer targets more genes, on average, compared to their mammalian counterparts suggesting higher versatility. These datasets and corresponding analysis represent a unique opportunity for the emerging field of comparative epigenomics, as well as animal and human biology and medical research involving species that are globally important food resources.

sample_organism:
Gallus gallus
Sus scrofa
Bos taurus

platform_organism:
Gallus gallus
Sus scrofa
Bos taurus

overall_design: H3K4me1 ChIP-seq in 8 tissues from 3 livestock species (2 adult male replicates per species)

first: Huaijun

first: Pablo

last: Ross


title: Epigenomic Landscape of Mouse Brain by Single Nucleus Methylation Sequencing [CEMBA181210_5C]

status: Public on Sep 25 2020

last: Bartlett

first: Jacinta

last: Lucero

last: Nery

first: Andrew

last: Aldridge

first: Rosa

last: Castanon

first: Yupeng

last: He

first: Huaming

first: Zhuzhu

first: Jingtian

first: Bing


title: Comparative functional genome annotation of livestock species identifies core amniote regulatory features and avian enhancer versatility (H3K4me3 ChIP-Seq)

overall_design: H3K4me3 ChIP-seq in 8 tissues from 3 livestock species (2 adult male replicates per species)

last: Zhou


title: Comparative functional genome annotation of livestock species identifies core amniote regulatory features and avian enhancer versatility (H3K27me3 ChIP-Seq)

overall_design: H3K27me3 ChIP-seq in 8 tissues from 3 livestock species (2 adult male replicates per species)


title: Epigenomic Landscape of Mouse Brain by Single Nucleus Methylation Sequencing [CEMBA181218_5F]

last: Chen

last: Zhang

last: Ren

first: Eran

last: Mukamel

first: M

last: Behrens


title: Comparative functional genome annotation of livestock species identifies core amniote regulatory features and avian enhancer versatility


title: Comparative functional genome annotation of livestock species identifies core amniote regulatory features and avian enhancer versatility (DNase-Hypersensitivity)

overall_design: DNase-seq in 8 tissues from chickens (2 adult male replicates per species)


title: Comparative functional genome annotation of livestock species identifies core amniote regulatory features and avian enhancer versatility (H3K27ac ChIP-Seq)

overall_design: H3K27ac ChIP-seq in 8 tissues from 3 livestock species (2 adult male replicates per species)


title: Comparative functional genome annotation of livestock species identifies core amniote regulatory features and avian enhancer versatility (CTCF ChIP-Seq)

overall_design: CTCF ChIP-seq in 8 tissues from 3 livestock species (2 adult male replicates per species)


title: Epigenomic Landscape of Mouse Brain by Single Nucleus Methylation Sequencing [CEMBA snm3C-seq]

status: Public on Oct 12 2020

first: Joseph

last: Ecker

summary: Illustrating the cellular architecture of the mammalian brain is critical to understanding its diverse functions and complex animal behaviors. With support from NIMH and NINDS as part of the BRAIN Initiative Cell Census Network (BICCN), the Center for Epigenomics of the Mouse Brain Atlas (CEMBA) applied single nucleus methylation sequencing in 118 (45 in the current release) brain funtional regions across the whole adult male P56 C57BL/6J mouse brain. In each major brain regions, we identified distinct cell clusters and formed them in a hierarchical taxonomy. These clusters include known primary brain cell types and possible sub-types. We use these data to identify the epigenomic characteristics and to define specific regulatory elements for each cell cluster. We integrate the single cell methylome with single cell gene expression and chromatin accessibility profiles from the same brain region to further identify potential enhancers and their corresponding genes for several neuronal cell types. By brain region spacial comparisons, we found spatial specificity among excitatory neuronal clusters within the same cortical layer. We identify brain-region-specific transcription factors that may regulate cortical region development of excitatory neurons. These data define the landscape of cell type and spatial heterogeneity in the mouse brain and the underlining regulatory epigenomic basis.

overall_design: This subseries consists of snm3C-seq data from hippocampus.

first: Hanqing

last: Liu

first: Ben

last: Clock

first: Jesse

last: Dixon


title: Comparative functional genome annotation of livestock species identifies core amniote regulatory features and avian enhancer versatility (RNA-Seq)

first: Colin

last: Kern

overall_design: RNA-seq in 8 tissues from 3 livestock species (2 adult male replicates per species)

last: Ross


title: Epigenomic Landscape of Mouse Brain by Single Nucleus Methylation Sequencing [CEMBA181206_5E]

first: Chongyuan

last: Luo

first: Angeline

last: Rivkin

first: Anna

last: Bartlett

last: Lucero


title: Comparative functional genome annotation of livestock species identifies core amniote regulatory features and avian enhancer versatility (ATAC-Seq)

sample_organism:
Sus scrofa
Bos taurus

platform_organism:
Sus scrofa
Bos taurus

overall_design: ATAC-seq in 8 tissues from 2 livestock species (2 adult male replicates per species)

first: Huaijun

first: Pablo


title: Gene expression in the nucleus accumbens shell of adult rats of both sexes after chronic exposure to delta9-tetrahydrocannabinol during adolescence

status: Public on Sep 19 2020

city: Madrid

first: Alejandro

last: Higuera-Matas

state: Madrid

address: Calle Juan del Rosal 10

department: Psychobiology

country: Spain

institute: Universidad Nacional de Educación a Distancia (UNED)

summary: Canabinoid exposure during adolescence  alters the rewarding properties of drugs of abuse by mechanisms that are not fully understood. The nucleus accumbens is a key node of the circuit mediating the rewarding effects of most drugs. Here, we present data on the differential gene expression in the nucleus accumbens shell in male and female Wistar rats (postnatal day 90) after exposure to THC (3 mg/kg i.p.) or vehicle (ethanol:cremophor:saline; 1:1:18; 2 mL/kg i.p.) during adolescence (postnatal day 28 to postnatal day 44; injections on alternate days). There were 96 DEGs in THC-males compared to VEH-males and 87 DEGs in the females’ comparison. Only nine of these DEGs were present in both the THC vs. VEH comparison in both sexes. Our results suggest that THC exposure during adolescence affects several families of genes that have important functions for brain development, behavior and synaptic plasticity and could explain, at least in part, the complex behavioral phenotype observed in adult individuals with exposure to cannabinoids during adolescence.

overall_design: Gene expression profiles in the nucleus accumbens shell of male and female adult rats (around postnatal day 90) with chronic exposure to THC or vehicle during adolescence.

first: Javier

last: Orihuel


title: Epigenomic Landscape of Mouse Brain by Single Nucleus Methylation Sequencing [CEMBA181204_4G]

overall_design: Apply snmC-seq2 to 118 brain functional regions to identify epigenomic landcape of the adult mouse brain, this subseries consists of one single nucleus methylation sequencing experiment of brain region (LSX).

first: Jacinta

last: Nery

first: Andrew

last: Aldridge

first: Rosa

last: Castanon

first: Yupeng

last: He

first: Huaming

last: Chen

first: Zhuzhu

last: Zhou


title: Epigenomic Landscape of Mouse Brain by Single Nucleus Methylation Sequencing [CEMBA181023_6B]

status: Public on Sep 23 2020

first: Joseph

last: Ecker

overall_design: Apply snmC-seq2 to 118 brain functional regions to identify epigenomic landcape of the adult mouse brain, this subseries consists of one single nucleus methylation sequencing experiment of brain region (SSp).

first: Hanqing

last: Liu

last: Zhang

first: Jingtian

first: Bing

last: Ren

first: Eran

last: Mukamel

first: M

last: Behrens


title: Epigenomic Landscape of Mouse Brain by Single Nucleus Methylation Sequencing [CEMBA190305_11E]

status: Public on Oct 09 2020

overall_design: Apply snmC-seq2 to 118 brain functional regions to identify epigenomic landcape of the adult mouse brain, this subseries consists of one single nucleus methylation sequencing experiment of brain region (CA).

first: Chongyuan

last: Luo

first: Angeline

last: Rivkin

first: Anna


title: Single-cell Transcriptomic Landscape of Human Blood Cells

status: Public on Sep 17 2020

city: Tianjin

first: xiaowei

last: xie

address: 288 Nanjing Road

country: China

institute: Institute of Hematology and Blood Diseases Hospital

summary: We profiled the transcriptomes of 7,643 human blood cells covering 32 immunophenotypic cell types across 21 healthy donors. We constructed the single-cell transcriptional atlas of blood cells on the basis of protein-coding genes and long noncoding RNAs (lncRNAs) respectively, and showed a high consistence between them. Notably, lncRNAs and novel transcription factors regulating hematopoietic cell differentiation were identified.

overall_design:
Single cell RNAseq for BM/PB-derived 32 blood cells, involving in the samples from GSE137864
Note from submitter: We stored the raw data in "Chinese Academy of Sciences". We still need to store our raw data into NCBI SRA, after we obtain the permit of China.

first: Ping

last: Zhu

first: Tao

last: Cheng


title: Epigenomic Landscape of Mouse Brain by Single Nucleus Methylation Sequencing [CEMBA181016_5H]

status: Public on Sep 22 2020

overall_design: Apply snmC-seq2 to 118 brain functional regions to identify epigenomic landcape of the adult mouse brain, this subseries consists of one single nucleus methylation sequencing experiment of brain region (PAL).

last: Bartlett

first: Jacinta

last: Lucero

last: Nery

first: Andrew


title: Epigenomic Landscape of Mouse Brain by Single Nucleus Methylation Sequencing [CEMBA181022_6B]

last: Aldridge

first: Rosa

last: Castanon

first: Yupeng

last: He


title: Epigenomic Landscape of Mouse Brain by Single Nucleus Methylation Sequencing [CEMBA190716_8J]

status: Public on Sep 21 2020

last: Ecker

overall_design: Apply snmC-seq2 to 118 brain functional regions to identify epigenomic landcape of the adult mouse brain, this subseries consists of one single nucleus methylation sequencing experiment of brain region (DG).

first: Huaming

last: Chen

first: Zhuzhu

last: Zhou


title: Epigenomic Landscape of Mouse Brain by Single Nucleus Methylation Sequencing [CEMBA190711_8J]

status: Public on Sep 20 2020

first: Joseph

first: Hanqing

last: Liu

last: Zhang

last: Ren


title: Epigenomic Landscape of Mouse Brain by Single Nucleus Methylation Sequencing [CEMBA181009_5G]

status: Public on Sep 18 2020

overall_design: Apply snmC-seq2 to 118 brain functional regions to identify epigenomic landcape of the adult mouse brain, this subseries consists of one single nucleus methylation sequencing experiment of brain region (PIR).

last: Luo

first: Jingtian

first: Bing

last: Mukamel

last: Behrens


title: Epigenomic Landscape of Mouse Brain by Single Nucleus Methylation Sequencing [CEMBA181008_5G]

last: Rivkin

first: Eran

first: M


title: Wnt/PCP-primed intestinal stem cells directly differentiate into enteroendocrine or Paneth cells

status: Public on Sep 11 2020

city: Garching

first: Maren

last: Büttner

address: Ingolstädter Landstr. 1

country: Germany

institute: Helmholtz Zentrum München

summary: We performed 7 single-cell RNAseq experiments to identify progenitor cell populations in the small intestine. To also capture rare intestinal cell populations such as stem cells and secretory cells we not only analyzed crypt cells from wildtype mice but also used two reporter mouse lines: i) the FltpZV/+ mouse line of which we mixed live crypt cells with Fltp Venus reporter (FVR) positive cells at different ratios and ii) Foxa2-Venus fusion (FVF) reporter mice. The FVF-enriched samples are part of another manuscript (link to GEO# will be provided). Using this FACS-based enrichment strategy, we could identify a Paneth cell-primed ISC population and potential progenitor populations for all intestinal lineages. To assess the role of Wnt/PCP signaling for enteroendocrine and Paneth cell differentiation, we performed 4 single-cell RNAseq experiments from crypt cells of Celsr1crsh/+; FltpZV/ZV compound mutant mice. When comparing control and mutant cells we found specific transcriptional alterations in the Paneth cell lineage.

overall_design: 7 single-cell RNA-seq experiments were performed using 10X Genomics technology to generate  single cell transcriptomic profiles of small intestinal epithelial crypt cells from control wildtype and FltpZV/+ mouse line. 4 samples single-cell RNA-seq experiments were performed using 10X Genomics technology to generate  single cell transcriptomic profiles of small intestinal epithelial crypt cells  from a Flattop (Fltp)-Venus-Reporter (FVR) Celsr1(crsh) hemizygous mouse line. Cells were sampled from the small intestine of adult mice. Cells were sorted to enrich for FVR positive cells.

first: Anika

last: Böttcher

first: Sophie

last: Tritschler

first: Mchael

last: Sterr

first: Alexandra

last: Aliluev

first: Lena

last: Oppenländer

first: Ingo

last: Burtscher

first: Steffen

last: Sass

first: Martin

last: Irmler

first: Johannes

last: Beckers

first: Christoph

last: Ziegenhain

first: Wolfgang

last: Enard

first: Andrea

middle: C

last: Schamberger

first: Fien

last: Verhamme

first: Oliver

last: Eickelberg

first: Fabian

middle: J

last: Theis

first: Heiko

last: Lickert


title: Epigenomic Landscape of Mouse Brain by Single Nucleus Methylation Sequencing [CEMBA190627_10F]

first: Joseph

last: Ecker

first: Hanqing

last: Liu

first: Chongyuan

last: Luo

first: Angeline

last: Rivkin

first: Anna

last: Bartlett

first: Jacinta

last: Lucero

last: Nery

first: Andrew

last: Aldridge

first: Rosa

last: Castanon

first: Yupeng

last: He

first: Huaming

last: Chen

first: Zhuzhu

last: Zhang

first: Jingtian

last: Zhou

first: Bing

last: Ren

first: Eran

last: Mukamel

first: M

last: Behrens


title: Epigenomic Landscape of Mouse Brain by Single Nucleus Methylation Sequencing [CEMBA190625_10E]

status: Public on Sep 14 2020


title: Epigenomic Diversity of Cortical Projection Neurons in the Mouse Brain

status: Public on Nov 16 2020

summary: Neuronal cell types are classically defined by their molecular properties, anatomy, and functions. While recent advances in single-cell genomics have led to high-resolution molecular characterization of cell type diversity in the brain, neuronal cell types are often studied out of the context of their anatomical properties. To better understand the relationship between molecular and anatomical features defining cortical neurons, we developed Epi-Retro-Seq, a method that combined retrograde labeling with single-nucleus DNA methylation sequencing to link epigenomic properties of cell types to neuronal projections. We profiled 16,971 single neocortical neurons from 63 cortico-cortical and cortico-subcortical long-distance projections. Our results revealed unique epigenetic signatures of projection neurons that correspond to their laminar and regional location and projection patterns.   The methylomes of 16,971 mouse neocortical neurons from 63 cortico-cortical (CC) and cortico-subcortical long-distance projections were analyzed using Epi-Retro-Seq, a method that combined retrograde tracing and single nucleus methylome sequencing.

overall_design: In Epi-Retro-Seq, the retrograde viral tracer rAAV2-retro-Cre is injected in the target region in an INTACT mouse, turning on Cre-dependent nuclear-GFP expression in neurons that project to the injected target, throughout the mouse brain. The brain is then sectioned into eighteen 600-micron coronal slices, and the brain regions of interest are mannually dissected from each slice. Nuclei are sampled from at least 4 mice (2 male and 2 female) for each projection target (except AI→pons - 2 male mice only). Nuclei from each of the dissected source regions are prepared, from which GFP+/NeuN+ nuclei (the GFP-labeled projection neurons) are isolated as single nuclei using fluorescence activated nuclei sorting (FANS) and assayed using snmC-Seq2 to profile their genome-wide DNA methylation signatures. We assayed approximately 384 nuclei from each projection (except the MOp→SSp projection from which 768 nuclei were assayed). Low-quality nuclei were removed.

first: Pengcheng

last: Tan

first: Yan

last: Pang

first: Elora

last: Williams

first: Cheng-Ta

last: Lee

first: Paula

last: A. Miyazaki

first: Minh

last: Vu

first: Lara

last: Boggeman

first: Conor

last: Fitzpatrick

middle: G

first: Mohammad

last: Rashid

first: Matthew

last: Jacobs

first: Tony

last: Ito

first: Bertha

last: Dominguez

first: Jared

middle: B

last: Smith

first: Carolyn

last: O'Connor

first: Kuo-Fen

first: Xin

last: Jin

first: Edward

last: Callaway


title: Epigenomic Landscape of Mouse Brain by Single Nucleus Methylation Sequencing [CEMBA180925_5E]

first: Joseph

last: Ecker

overall_design: Apply snmC-seq2 to 118 brain functional regions to identify epigenomic landcape of the adult mouse brain, this subseries consists of one single nucleus methylation sequencing experiment of brain region (CP).

first: Hanqing

last: Liu

first: Chongyuan

last: Luo

first: Angeline

last: Rivkin

first: Anna

last: Bartlett

first: Jacinta

last: Lucero

last: Nery

first: Andrew

last: Aldridge

first: Rosa

last: Castanon

first: Yupeng

last: He

first: Huaming

last: Chen

first: Zhuzhu

last: Zhang

first: Jingtian

last: Zhou

first: Bing

last: Ren

first: Eran

last: Mukamel

first: M

last: Behrens


title: Epigenomic Landscape of Mouse Brain by Single Nucleus Methylation Sequencing [CEMBA180917_4G]

status: Public on Sep 10 2020


title: Smaller stature in childhood following assisted reproductive technologies (ART) is not explained by parental or gestational factors, early childhood environment, or fetal DNA methylation [GUSTO_buffy_coat]

status: Public on Sep 16 2020

city: Singapore

first: Jonathan

middle: Yinhao

last: Huang

state: « choose one »

address: 30 Medical Drive

country: Singapore

institute: Singapore Institute for Clinical Sciences

type: Methylation profiling by genome tiling array

summary: As part of an investigation on contributors to offspring size following assisted reproduction, we investigated maternal mid-/late-pregnancy peripheral blood buffy coat DNA methylation at 240 CpGs previously associated with maternal pregnancy morbidity or offspring growth across various tissues. Illumina Infinium MethylationEPIC BeadChip was used to obtain DNA methylation profiles in previously frozen buffy coat samples from 70 women who conceived via assisted reproduction technologies and gave live births and 845 women who spotaneously conceived and gave live births.

overall_design: GUSTO (Growing Up In Singapore Towards healthy Outcomes; n = 1178) is a nationally-representative pregnancy and birth cohort with continuous follow-up from early gestiation through 10 years. Illumina Infinium MethylationEPIC BeadChip was used to evaluate genome-wide DNA methylation in maternal peripheral blood buffy coat in mid-/late- pregnancy (~26-28 gestational weeks) for all subjects with sufficient sample quantities. Genome-wide DNA methylation in fetal cord tissue was profiled separately by Illumina HumanMethylation 450K for all live births with sufficient sample quantities. These data are reported in a a separate series.


title: Epigenomic Landscape of Mouse Brain by Single Nucleus Methylation Sequencing [CEMBA190716_8E]

last: Ecker


title: Smaller stature in childhood following assisted reproductive technologies (ART) is not explained by parental or gestational factors, early childhood environment, or fetal DNA methylation [GUSTO_cord_tissue]

status: Public on Sep 15 2020

summary: As part of an investigation on contributors to offspring size following assisted reproduction, we investigated fetal cord tissue DNA methylation at 281 CpGs previously associated with maternal pregnancy morbidity or offspring growth across various tissues. The Illumina HumanMethylation450 BeadChip was used to obtain DNA methylation profiles in previously frozen cord tissues samples from 69 assisted reproduction-conceived and 950 spotaneously conceived live births.

overall_design: GUSTO (Growing Up In Singapore Towards healthy Outcomes; n = 1178) is a nationally-representative pregnancy and birth cohort with continuous follow-up from early gestiation through 10 years. Illumina HumanMethylation 450K was used to evaluate genome-wide DNA methylation in fetal cord tissue samples for all live births with sufficient sample quantities. Genome-wide DNA methylation in maternal mid-/late- pregnancy peripheral blood buffy coat was profiled separately by Illumina Infinium MethylationEPIC BeadChip for women with sufficient sample quantities. These data are reported in a a separate series.


title: Epigenomic Landscape of Mouse Brain by Single Nucleus Methylation Sequencing [CEMBA190711_8E]

last: Liu


title: Epigenomic Landscape of Mouse Brain by Single Nucleus Methylation Sequencing [CEMBA190627_10E]

last: Luo


title: Epigenomic Landscape of Mouse Brain by Single Nucleus Methylation Sequencing [CEMBA181015_5H]

last: Rivkin


title: Smaller stature in childhood following assisted reproductive technologies (ART) is not explained by parental or gestational factors, early childhood environment, or fetal DNA methylation

overall_design: Refer to individual Series


title: Epigenomic Landscape of Mouse Brain by Single Nucleus Methylation Sequencing [CEMBA181002_5C]

status: Public on Sep 13 2020

overall_design: Apply snmC-seq2 to 118 brain functional regions to identify epigenomic landcape of the adult mouse brain, this subseries consists of one single nucleus methylation sequencing experiment of brain region (SSs).

last: Bartlett


title: Epigenomic Landscape of Mouse Brain by Single Nucleus Methylation Sequencing [CEMBA180904-5J]

status: Public on Sep 08 2020

last: Lucero


title: Radiation-Induced DNA Damage and Repair Effects on 3D Genome Organization

status: Public on Sep 04 2020

city: Knoxville

first: Rachel

middle: Patton

last: McCord

state: TN

address: 1311 Cumberland Ave

department: BCMB

institute: University of Tennessee,Knoxville

summary: We investigate the impact of DNA damage response and repair on 3D genome folding using Hi-C experiments on wild type cells and ataxia telangiectasia mutated (ATM) patient cells. Fibroblasts, lymphoblasts, and ATM-deficient fibroblasts were irradiated with 5 Gy X-rays and Hi-C was performed after 30 minutes, 24 hours, or 5 days after irradiation.

overall_design: Examination of the effects of X-rays on 6 different cell types

first: Jacob

middle: T

last: Sanders

first: Trevor

middle: F

last: Freeman

first: Yang

last: Xu

first: Rosela

last: Golloshi

first: Mary

last: Stallard

first: Ashtyn

last: Hill

first: Rebeca

middle: S

last: Martin

first: Adayabalam

last: Balajee

middle: P


title: Single-cell transcriptome landscape of adult HSPC

status: Public on Sep 02 2020

first: xiaowei

last: xie

summary: Single-cell transcriptome landscape of HSPCs from the bone marrow of 3 healthy donors

overall_design: Single cell RNAseq for BM-derived HSPCs from 3 healthy donors

first: Ping

last: Zhu

first: Tao

last: Cheng


title: Epigenomic Landscape of Mouse Brain by Single Nucleus Methylation Sequencing [CEMBA180806_4H]

status: Public on Sep 07 2020

first: Joseph

last: Ecker

first: Hanqing

last: Liu

first: Chongyuan

first: Angeline

first: Anna

first: Jacinta

last: Nery

first: Andrew

last: Aldridge

first: Rosa

last: Castanon

first: Yupeng

last: He

first: Huaming

last: Chen

first: Zhuzhu

last: Zhang

first: Jingtian

last: Zhou

last: Ren

last: Mukamel

last: Behrens


title: Epigenomic Landscape of Mouse Brain by Single Nucleus Methylation Sequencing [CEMBA180910_5J]

last: Luo

last: Rivkin

last: Bartlett

last: Lucero

first: Bing

first: Eran

first: M


title: Epigenomic Landscape of Mouse Brain by Single Nucleus Methylation Sequencing [CEMBA180426-8B]


title: Epigenomic Landscape of Mouse Brain by Single Nucleus Methylation Sequencing [CEMBA180911_4H]

status: Public on Sep 09 2020


title: Florigen family chromatin recruitment, competition and targets [ChIP-Seq]

status: Public on Sep 01 2020

city: Philadelphia

first: Doris

last: Wagner

state: PA

address: 103G Carolyn Lynch Laboratory

department: Department of Biology

institute: University of Pennsylvania

summary: This study identified direct targets of TFL1 and FD and showed that TFL1 is recruited to the chromatin by FD. We performed ChIP-seq using anti-GFP antibodies in gTFL1-GFP tfl1-1, gTFL1-GFP fd-1 and controls (nontransgenic plants). We used anti-GUS antibodies for gFD-GUS fd-1. ChIP was conducted on dissected, non-bolted, inflorescences from 42-day-old short-day-grown Arabidopsis thaliana.

overall_design: Identification of binding sites for FD and TFL1 in axillary buds in wildtype Arabidopsis Col-0 short-day grown plants. Two biological ChIP replicates were sequence for FD fd and TFL1 fd, four for TFL1 tfl1; two anti GFP mock (controls) each for wild type and fd. Four inputs were sequenced.

first: Samantha

last: Klasfeld

first: Yang

last: Zhu


title: Epigenomic Landscape of Mouse Brain by Single Nucleus Methylation Sequencing [CEMBA190625_10F]

first: Joseph

last: Ecker

first: Hanqing

last: Liu

last: Nery


title: Increasing the cellular (pp)pGpp level is associated with activation of stress response genes in Staphylococcus aureus

city: Tübingen

first: Christiane

last: Wolz

address: Elfriede-Aulhorn-Strasse 6

institute: University Tübingen

summary: The stringent response is characterized by the synthesis of the messenger molecules pppGpp, ppGpp or pGpp (collectively designated (pp)pGpp). The phenotypic consequences resulting from (pp)pGpp accumulation vary among species and can be mediated by different underlying mechanisms. Most genome-wide analyses were performed under stress conditions, which often mask the immediate effects of (pp)pGpp mediated regulatory circuits.       In Staphylococcus aureus (pp)pGpp can be synthesized via the RelA-SpoT- homologue (RSHSau) upon amino-acid limitation or via one of the two small (p)ppGpp synthetases RelP or RelQ upon cell-wall stress. We used RNA-seq to compare global effects in response to transcriptional induction of the synthetase domain of RSH (RSH- Syn) or RelQ without the need to apply additional stress conditions. We found a significant upregulation of iron and oxidative stress genes. Simultanously, virulence genes psms were upregulated independ of the its regulator Agr. Based and these RNA-Seq results we created mutants of the regulators  PerR, Fur and SarA which are associated with the regulation of oxidative stress and iron

overall_design: We compared the trascriptional downstream effects of (pp)pGpp by transcriptional induction of RSH-Syn and RelQ by RNA Seq, triplicates, Illumina  Next Seq 500 system,

first: Petra

last: Horvatek


title: Epigenomic Landscape of Mouse Brain by Single Nucleus Methylation Sequencing [CEMBA180430-8B]

status: Public on Sep 05 2020

overall_design: Apply snmC-seq2 to 118 brain functional regions to identify epigenomic landcape of the adult mouse brain, this subseries consists of one single nucleus methylation sequencing experiment of brain region (SSp).

first: Chongyuan

first: Angeline

first: Anna

first: Jacinta

last: Aldridge

last: Castanon

last: He

last: Chen

last: Zhang


title: Epigenomic Landscape of Mouse Brain by Single Nucleus Methylation Sequencing [CEMBA180605_5D]

overall_design: Apply snmC-seq2 to 118 brain functional regions to identify epigenomic landcape of the adult mouse brain, this subseries consists of one single nucleus methylation sequencing experiment of brain region (MOp).

last: Luo

first: Andrew

first: Rosa

first: Yupeng

first: Huaming

last: Zhou

last: Ren

last: Mukamel

last: Behrens


title: Florigen family chromatin recruitment, competition and targets [RNA-Seq]

last: Wagner

summary: This study identified genes that re-upregulated in far-red enriched photoperiod in the wild type or tfl1-1, but not in ft-10 (FT-dependent photoinduction). We performed RNA seq on tfl1-1, wild type and ft-10 grown for 42 days in short-day conditions and treated for 24 hours with far-red enriched photoinduction (24 hr FRP) or grown for 43 days in short-day conditions (no FRP). RNA was isolated from trimmed and dissected non-bolted inflorescences.

overall_design: We sequenced three biological replicates per genotype and treatment and analyzed two biological replicates per condition for differential expression.

last: Klasfeld


title: FD-seq: Droplet-based RNA sequencing of fixed single cells

status: Public on Aug 28 2020

first: Hoang Van

last: Phan

address: 5640 S Ellis Ave

department: Priztker School of Molecular Engineering

institute: The University of Chicago

summary: Current high-throughput single-cell RNA sequencing (scRNA-seq) methods are incompatible with paraformaldehyde (PFA) fixation, a common cell/tissue preservation and viral inactivation technique, which has prevented transcriptomic analysis of rare cells that require protein staining and enrichment. Here we present FD-seq, a method for high-throughput RNA sequencing of PFA-fixed, stained and FACS-sorted single cells. We used FD-seq to address two important questions in virology. First, by analyzing a rare population of cells supporting herpesvirus reactivation, we identified TMEM119 to mediate reactivation of Kaposi’s sarcoma-associated herpesvirus (KSHV), a tumor virus. Second, we studied the innate immune activation in cells infected with the coronavirus OC43, which causes the common cold and also serves as a safer model pathogen for SARS-CoV-2 studies. We found that pro-inflammatory cytokine induction, which is a major contributor to the severe pathogenicity in SARS-CoV-2-infected individuals, is primarily driven by uninfected or lowly infected bystander cells that are exposed to the virus but fail to express high level of viral genes. FD-seq is a simple method that is suitable for characterizing the transcriptome of rare cell populations of interest, and for studying high-containment biological samples such as SARS-CoV-2-infected cells after PFA inactivation.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: KSHV reactivation is chemically induced, and the mRNA from single reactivated and non-reactivated cells are sequenced. Bulk RNA-seq was performed to identify the mechanism of TMEM119-induced reactivation. OC43 infected and mock infected cells were sequenced to identify subpopulation of bystander cells. The performance of FD-seq was also compared to the standard Drop-seq method for methanol-fixed cells.

first: Hoang

middle: V


title: Epigenomic Landscape of Mouse Brain by Single Nucleus Methylation Sequencing [CEMBA180529_5B]

status: Public on Aug 31 2020

last: Ecker

summary: Illustrating the cellular architecture of the mammalian brain is critical to understanding its diverse functions and complex animal behaviors. With support from NIMH and NINDS as part of the BRAIN Initiative Cell Census Network (BICCN), the Center for Epigenomics of the Mouse Brain Atlas (CEMBA) applied single nucleus methylation sequencing in 118 brain funtional regions across the whole adult male P56 C57BL/6J mouse brain. In each major brain regions, we identified distinct cell clusters and formed them in a hierarchical taxonomy. These clusters include known primary brain cell types and possible sub-types. We use these data to identify the epigenomic characteristics and to define specific regulatory elements for each cell cluster. We integrate the single cell methylome with single cell gene expression and chromatin accessibility profiles from the same brain region to further identify potential enhancers and their corresponding genes for several neuronal cell types. By brain region spacial comparisons, we found spatial specificity among excitatory neuronal clusters within the same cortical layer. We identify brain-region-specific transcription factors that may regulate cortical region development of excitatory neurons. These data define the landscape of cell type and spatial heterogeneity in the mouse brain and the underlining regulatory epigenomic basis.

last: Liu

last: Rivkin

last: Bartlett

last: Lucero

first: Zhuzhu

first: Jingtian

first: Bing

first: Eran

first: M


title: Transcriptomics analysis of mesenteric adipose tissue from Crohn's disease patients and healthy controls [RNA-seq]

city: West Hollywood

first: AGCT

last: Core

address: 8687 Melrose Ave, PDC B230

department: BMS

institute: Cedars Sinai Medical Center

summary: A feature of Crohn's disease is the extra-intestinal manifestation of creeping fat, defined as expansion of mesenteric adipose tissue around the inflamed and fibrotic ileum. In comparison to healthy controls, we found that the greatest transcriptional changes in creeping fat are functions related to immune response to bacterial products.

overall_design: We compared the transcriptional activity of creeping fat from four Crohn's disease patients and healthy mesenteric adipose tissues from ileal controls (IRB# Pro00048577).

first: Connie

middle: W

last: Ha

first: Suzanne

last: Devkota

first: Yizhou

last: Wang


title: Epigenomic Landscape of Mouse Brain by Single Nucleus Methylation Sequencing [CEMBA180514_5B]

status: Public on Aug 27 2020

first: Joseph

first: Hanqing

first: Chongyuan

last: Luo

first: Angeline

first: Anna

last: Nery

last: Aldridge

last: Castanon

last: He

last: Chen

last: Zhang


title: Epigenomic Landscape of Mouse Brain by Single Nucleus Methylation Sequencing [CEMBA180612_5D]

first: Jacinta

first: Andrew

first: Rosa

first: Yupeng

first: Huaming

last: Zhou

last: Ren

last: Mukamel

last: Behrens


title: Evolutionary transcriptomics implicates HAND2 in the origins of implantation and regulation of gestation length

status: Public on Aug 26 2020

city: Buffalo

first: Vincent

middle: J.

last: Lynch

state: NY

address: 551 Cooke Hall

department: Department of Biological Sciences

institute: University at Buffalo, SUNY

summary: The developmental origins and evolutionary histories of cell types, tissues and organ systems contribute to the ways in which their dysfunction leads to disease. In mammals for example, the nature and extent of maternal-fetal interactions, how those interactions develop, and their evolutionary history likely influence diseases of pregnancy such as infertility and preterm birth. Here we show genes that evolved to be expressed at the maternal-fetal interface in Eutherian (‘Placental') mammals play essential roles in the evolution of pregnancy and are associated with immune system disorders and preterm birth. Among these genes is the transcription factor HAND2, which suppresses estrogen signaling, an innovation of Eutherians, thereby allowing blastocyst implantation. We found that HAND2 is dynamically expressed in the decidua throughout the menstrual cycle and pregnancy, gradually decreasing to reach a low at term. HAND2 regulates a small but distinct set of target genes in endometrial stromal fibroblasts including the cytokine IL15, which was also dynamically expressed throughout the menstrual cycle and gestation, and promoted the migration of natural killer cells and extravillous cytotrophoblasts. Remarkably, we found that the HAND2 promoter loops to a distal enhancer containing SNPs implicated in the regulation of gestation length and birth weight. Collectively, these data connect HAND2 expression at the maternal-fetal interface with the evolution of implantation and gestation length regulation, and preterm birth.

overall_design: mRNA-Seq in ESF cells treated with negative control siRNAs or siRNA targeting human HAND2.

last: Marinic

first: V


title: Epigenomic Landscape of Mouse Brain by Single Nucleus Methylation Sequencing [CEMBA180424_7B]

middle: R

last: Ecker

last: Liu

last: Rivkin

last: Bartlett

last: Lucero

first: Zhuzhu

first: Jingtian

first: Bing

first: Eran

first: M


title: Translocation of Viable Gut Microbiota to Mesenteric Adipose Drives Formation of Creeping Fat in Humans

status: Public on Aug 25 2020

city: Quechee

first: Michael

last: Steinbaugh

state: VT

address: PO Box 1520

institute: Acid Genomics

summary: A mysterious feature of Crohn’s disease (CD) is the extra-intestinal manifestation of "creeping fat" (CrF), defined as expansion of mesenteric adipose tissue around the inflamed and fibrotic intestine. In the current study, we explored whether microbial translocation in human intestinal inflammation serves as a central cue for CrF development. We discovered a subset of mucosal-associated gut bacteria that consistently translocated and remained viable in CrF in CD ileal surgical resections. We identified Clostridium innocuum as a signature of this consortium with strain variation between the mucosa and adipose. Single-cell RNA sequencing characterized CrF as both pro-fibrotic and pro-adipogenic with a rich milieu of activated immune cells responding to microbial stimuli, which we confirm in gnotobiotic mice colonized with C. innocuum. Ex vivo validation of expression patterns suggests C. innocuum stimulates tissue remodeling via M2 macrophages leading to an adipose tissue barrier that prevents further dissemination of bacteria.

overall_design: Single-cell RNA-seq analysis of stromal vascular cells (SVCs) isolated from primary adipose tissue. SureCell samples: healthy and inflamed tissue from 3 Crohn's disease patients, 2 ulcerative colitis patients; Chromium samples: 2 Crohn's disease patients, 2 non-IBD controls.

first: Connie

last: Ha

first: Anthony

last: Martin

first: Gregory

middle: D

last: Sepich-Poore

first: Baochen

last: Shi

first: Yizhou

last: Wang

first: Kenneth

last: Gouin

last: Humphrey

first: Karenina

last: Sanders

first: Yasiru

last: Ratnayake

first: Kelvin

last: Chan

first: Gustaf

last: Hendrick

first: Juan

last: Rafael Caldera

first: Christian

last: Arias

first: Jacob

middle: E

last: Moskowitz

first: Shannan

last: Ho Sui

first: Shaohong

last: Yang

first: David

last: Underhill

first: Matthew

last: Brady

first: Simon

last: Knott

first: Kelly

last: Kaihara

first: Huiying

last: Li

first: Dermot

last: McGovern

first: Rob

last: Knight

first: Phillip

last: Fleshner

first: Suzanne

last: Devkota


title: Epigenomic Landscape of Mouse Brain by Single Nucleus Methylation Sequencing [CEMBA180412_3D]

first: Joseph

last: Ecker

overall_design: Apply snmC-seq2 to 118 brain functional regions to identify epigenomic landcape of the adult mouse brain, this subseries consists of one single nucleus methylation sequencing experiment of brain region (AI).

first: Hanqing

last: Liu

first: Chongyuan

last: Luo

first: Angeline

last: Rivkin

first: Anna

last: Bartlett

first: Jacinta

last: Lucero

last: Nery

first: Andrew

last: Aldridge

first: Rosa

last: Castanon

first: Yupeng

last: He

first: Huaming

last: Chen

first: Zhuzhu

last: Zhang

first: Jingtian

last: Zhou

first: Bing

last: Ren

first: Eran

middle: A

last: Mukamel

first: M

middle: M

last: Behrens


title: Epigenomic Landscape of Mouse Brain by Single Nucleus Methylation Sequencing [CEMBA180417_4C]


title: Epigenomic Landscape of Mouse Brain by Single Nucleus Methylation Sequencing [CEMBA180501_3B]

overall_design: Apply snmC-seq2 to 118 brain functional regions to identify epigenomic landcape of the adult mouse brain, this subseries consists of one single nucleus methylation sequencing experiment of brain region (MOs).


title: Epigenomic Landscape of Mouse Brain by Single Nucleus Methylation Sequencing [CEMBA180419_4C]


title: Epigenomic Landscape of Mouse Brain by Single Nucleus Methylation Sequencing [CEMBA180423_7B]


title: Epigenomic Landscape of Mouse Brain by Single Nucleus Methylation Sequencing [CEMBA180410_2C]


title: Epigenomic Landscape of Mouse Brain by Single Nucleus Methylation Sequencing [CEMBA180409_2C]


title: Epigenomic Landscape of Mouse Brain by Single Nucleus Methylation Sequencing [CEMBA180329_4F]

overall_design: Apply snmC-seq2 to 118 brain functional regions to identify epigenomic landcape of the adult mouse brain, this subseries consists of one single nucleus methylation sequencing experiment of brain region (PIR).


title: Epigenomic Landscape of Mouse Brain by Single Nucleus Methylation Sequencing [CEMBA180319_2D]

status: Public on Aug 24 2020


title: Epigenomic Landscape of Mouse Brain by Single Nucleus Methylation Sequencing [CEMBA180416_3D]


title: Epigenomic Landscape of Mouse Brain by Single Nucleus Methylation Sequencing [CEMBA180402_4F]


title: Epigenomic Landscape of Mouse Brain by Single Nucleus Methylation Sequencing [CEMBA180313_2D]


title: Epigenomic Landscape of Mouse Brain by Single Nucleus Methylation Sequencing [CEMBA180320_3E]


title: Transcriptomics analysis of mesenteric adipose tissue from Crohn's disease patients and healthy controls

first: AGCT

last: Core

summary: This SuperSeries is composed of the SubSeries listed below.


title: Epigenomic Landscape of Mouse Brain by Single Nucleus Methylation Sequencing [CEMBA180312_3B]

last: Ecker


title: Epigenomic Landscape of Mouse Brain by Single Nucleus Methylation Sequencing [CEMBA180306_2B]

last: Liu


title: Epigenomic Landscape of Mouse Brain by Single Nucleus Methylation Sequencing [CEMBA180405_3F]

overall_design: Apply snmC-seq2 to 118 brain functional regions to identify epigenomic landcape of the adult mouse brain, this subseries consists of one single nucleus methylation sequencing experiment of brain region (ACB).

last: Luo


title: Epigenomic Landscape of Mouse Brain by Single Nucleus Methylation Sequencing [CEMBA180326_3E]

last: Rivkin


title: Epigenomic Landscape of Mouse Brain by Single Nucleus Methylation Sequencing [CEMBA180222_2E]

status: Public on Aug 23 2020

overall_design: Apply snmC-seq2 to 118 brain functional regions to identify epigenomic landcape of the adult mouse brain, this subseries consists of one single nucleus methylation sequencing experiment of brain region (AON).

last: Bartlett


title: Epigenomic Landscape of Mouse Brain by Single Nucleus Methylation Sequencing [CEMBA180403_2D]

last: Lucero


title: Epigenomic Landscape of Mouse Brain by Single Nucleus Methylation Sequencing [CEMBA180305_2B]

last: Nery


title: SEAM is a spatial single nuclear metabolomics method for dissecting tissue microenvironment

status: Public on Aug 22 2020

city: Beijing

first: Qiming

address: No. 30, Shuangqing Road, Haidian District

institute: Tsinghua University

summary: We report a method for analyzing spatial metabolomics at single cell level. In human fibrotic liver samples, we identified a novel hepatocyte subpopulation via SEAM and spatial transcriptomics using modified protocol of Geo-sea. For Geo-seq, we generated cDNA libraries from Hepa69-high (Proximal), Hepa69-low (Distal) and Fibrotic (FB) regions. The differential gene expression analysis between Hepa69-high and Hepa69-low indicates that genes from solute carrier transporter families were elevated in Hepa69-high group.

overall_design: Selected regions corresponding to three subpopulations (Hepa69-high (Proximal), Hepa69-low (Distal) and Fibrotic regions.) identified by SEAM were collected for Geo-seq.

first: Yang

first: Michael

middle: Q


title: Epigenomic Landscape of Mouse Brain by Single Nucleus Methylation Sequencing [CEMBA180220_2E]

first: Joseph

first: Hanqing

first: Chongyuan

last: Aldridge


title: Epigenomic Landscape of Mouse Brain by Single Nucleus Methylation Sequencing [CEMBA180227_1A]

first: Angeline

first: Anna

first: Jacinta

last: Castanon


title: Epigenomic Landscape of Mouse Brain by Single Nucleus Methylation Sequencing [CEMBA180212_1C]

first: Andrew

first: Rosa

first: Yupeng

last: He


title: Epigenomic Landscape of Mouse Brain by Single Nucleus Methylation Sequencing [CEMBA180213_1B]

overall_design: Apply snmC-seq2 to 118 brain functional regions to identify epigenomic landcape of the adult mouse brain, this subseries consists of one single nucleus methylation sequencing experiment of brain region (ORB).

first: Huaming

last: Chen

first: Zhuzhu

first: Jingtian


title: Epigenomic Landscape of Mouse Brain by Single Nucleus Methylation Sequencing [CEMBA180208_1C]

last: Zhang

first: Bing

first: Eran

first: M


title: Epigenomic Landscape of Mouse Brain by Single Nucleus Methylation Sequencing [CEMBA180206_4A]

overall_design: Apply snmC-seq2 to 118 brain functional regions to identify epigenomic landcape of the adult mouse brain, this subseries consists of one single nucleus methylation sequencing experiment of brain region (ACA,PL,ILA).

last: Zhou


title: Epigenomic Landscape of Mouse Brain by Single Nucleus Methylation Sequencing [CEMBA180122_2A]

status: Public on Aug 21 2020

last: Ren


title: Epigenomic Landscape of Mouse Brain by Single Nucleus Methylation Sequencing [CEMBA180129_3A]

last: Mukamel


title: Epigenomic Landscape of Mouse Brain by Single Nucleus Methylation Sequencing [CEMBA180205_4A]

last: Behrens


title: Epigenomic Landscape of Mouse Brain by Single Nucleus Methylation Sequencing [CEMBA180119_1B]


title: Epigenomic Landscape of Mouse Brain by Single Nucleus Methylation Sequencing [CEMBA180130_3A]


title: Epigenomic Landscape of Mouse Brain by Single Nucleus Methylation Sequencing [CEMBA180111_4E]


title: Epigenomic Landscape of Mouse Brain by Single Nucleus Methylation Sequencing [CEMBA171214_4D]

status: Public on Aug 20 2020

overall_design: Apply snmC-seq2 to 118 brain functional regions to identify epigenomic landcape of the adult mouse brain, this subseries consists of one single nucleus methylation sequencing experiment of brain region (CP).


title: Epigenomic Landscape of Mouse Brain by Single Nucleus Methylation Sequencing [CEMBA180110_4E]


title: Epigenomic Landscape of Mouse Brain by Single Nucleus Methylation Sequencing [CEMBA180109_3F]


title: Epigenomic Landscape of Mouse Brain by Single Nucleus Methylation Sequencing [CEMBA180123_2A]


title: Epigenomic Landscape of Mouse Brain by Single Nucleus Methylation Sequencing [CEMBA171219_4D]


title: GATA4 genome binding targets in adult mouse stomach

status: Public on Aug 13 2020

city: Milwaukee

first: Michele

last: Battle

state: WI

address: 8701 Watertown Plank Rd

department: Cell Biology, Neurobiology, and Anatomy

institute: Medical College of Wisconsin

summary: GATA4 facilitates its function as a transcriptional regulator by binding to promoter and enhancer regions of target genes in the glandular stomach.

overall_design: Sequencing of GATA4 bound chromatin in mouse stomach.

first: Ann

last: DeLaForest


title: GATA4 regulates epithelial morphogenesis in the developing mouse stomach to promote establishment of a simple columnar epithelium

status: Public on Aug 17 2020

overall_design: Refer to individual Series


title: Identification and Characterization of the Epigenome and Transcriptome in Human Neonates

status: Public on Aug 09 2020

first: Yong

last: Peng

state: IL

address: 929 E 57th Street

department: Department of Chemistry

institute: University of Chicago

summary: We performed reduced-representation bisulfite sequencing (RRBS) on 137 umbilical cord blood (UCB) samples and 158 parental peripheral blood (PPB) samples from nuclear families with either singletons or twins. The samples were classified into five groups based on the mode of conception: spontaneous (CTRL), IVF-ET, IVF-FET, ICSI-ET and ICSI-FET. There were no significant differences in the clinical features of the neonates among the different groups; in addition, maternal ages were under 35 years old and parental body mass index (BMI) values were comparable in general. In addition, we performed chromatin immunoprecipitation sequencing (ChIP-seq) on 33 UCB samples to examine histone modifications (H3K4me1, H3K4me3, H3K27ac, and H3K27me3) and RNA sequencing (RNA-seq) on 32 UCB samples to examine the transcriptomes of neonates.

overall_design: RRBS, ChIP-seq (H3K4me1, H3K4me3, H3K27ac, H3K27me3), and RNA-seq in umbilical cord blood of neonates and peripheral blood of their parents.

first: Wei

first: Xinyi

last: Ma

first: Siming

last: Kong

first: Shuangyan

last: Tang

first: Wenxin

first: Yang

last: Wang

first: Liying

last: Yan

first: Jie

last: Qiao


title: Epigenomic Landscape of Mouse Brain by Single Nucleus Methylation Sequencing [CEMBA171212_4B]

first: Joseph

last: Ecker

address: 10010 North Torrey Pines Road

institute: HHMI-Salk-Institute

overall_design: Apply snmC-seq2 to 118 brain functional regions to identify epigenomic landcape of the adult mouse brain, this subseries consists of one single nucleus methylation sequencing experiment of brain region (MOp).

first: Hanqing

last: Liu

first: Chongyuan

last: Luo

first: Angeline

last: Rivkin

first: Anna

last: Bartlett

first: Jacinta

last: Lucero

last: Nery

first: Andrew

last: Aldridge

first: Rosa

last: Castanon

first: Yupeng

first: Huaming


title: Enhancer-associated H3K4 methylation safeguards in vitro germline competence [scRNA-seq]

status: Public on Jul 27 2020

city: Santander

first: Alvaro

last: Rada-Iglesias

state: Cantabria

address: Albert Einstein 22, PCTCAN

institute: Institute of Biomedicine and Biotechnology of Cantabria (IBBTEC), CSIC/University of Cantabria

summary: Germline specification in mammals occurs through an inductive process whereby competent cells in the post-implantation epiblast differentiate into primordial germ cells (PGC). The intrinsic factors that endow epiblast cells with the competence to respond to germline inductive signals remain unknown. Single-cell RNA sequencing across multiple stages of an in vitro PGC-like cells (PGCLC) differentiation system shows that PGCLC genes initially expressed in the naïve pluripotent stage become homogeneously dismantled in germline competent epiblast like-cells (EpiLC). In contrast, the decommissioning of enhancers associated with these germline genes is incomplete. Namely, a subset of these enhancers partly retain H3K4me1, accumulate less heterochromatic marks and remain accessible and responsive to transcriptional activators. Subsequently, as in vitro germline competence is lost, these enhancers get further decommissioned and lose their responsiveness to transcriptional activators. Importantly, using H3K4me1 deficient cells, we show that the loss of this histone modification reduces the germline competence of EpiLC and decreases PGCLC differentiation efficiency. Our work suggests that, although H3K4me1 might not be essential for enhancer function, it can facilitate the (re)activation of enhancers and the establishment of gene expression programs during specific developmental transitions.

overall_design: ChIP-seq, ATAC-seq, genome-wide bisulftie sequencing, 4C-seq, RNA-seq and single cell RNA-seq from different stages of the PGCLC differentiation.

first: Tore

last: Bleckwehl


title: Epigenomic Landscape of Mouse Brain by Single Nucleus Methylation Sequencing [CEMBA171207_3C]

last: He

last: Chen

first: Zhuzhu

last: Zhang

first: Jingtian

last: Zhou

first: Bing

last: Ren

first: Eran

last: Mukamel

first: M

last: Behrens


title: Gene Expression in the developing hindstomach and forestomach of wild type and GATA4 conditional knock out and knock in embryonic mice

first: Michele

last: Battle

summary: Gene expression was compared between wild type forestomach and hindstomach epithelial cells at embryonic day E14.5. Gene expression was compared between GATA4 knock out hindstomach epithelial cells and wild type hindstomach epithelial cells at embryonic day E14.5. Gene expression was compared between GATA4 knock in forestomach epithelial cells and wild type forestomach epithelial cells at embryonic day E14.5.

overall_design: Sequencing of embryonic forestomach and hindstomach epithelial cells from wild type and GATA4 knock out and GATA4 knock in embryonic stomachs at E14.5.

first: Ann

last: DeLaForest


title: Epigenomic Landscape of Mouse Brain by Single Nucleus Methylation Sequencing [CEMBA180226_1A]

first: Joseph

last: Ecker

summary: Illustrating the cellular architecture of the mammalian brain is critical to understanding its diverse functions and complex animal behaviors. With support from NIMH and NINDS as part of the BRAIN Initiative Cell Census Network (BICCN), the Center for Epigenomics of the Mouse Brain Atlas (CEMBA) applied single nucleus methylation sequencing in ~95,000 single nucleus from 38 mice rostral brain functional regions and structures (Apr. 2019). In each major brain regions (isocortex, striatum, pallidum, hippocampus, and olfactory bulb), we identified distinct cell clusters and formed them in a hierarchical taxonomy. These clusters include known primary brain cell types and possible sub-types. We use these data to identify the epigenomic characteristics and to define specific regulatory elements for each cell cluster. We integrate the single cell methylome with single cell gene expression and chromatin accessibility profiles from the same brain region to further identify potential enhancers and their corresponding genes for several neuronal cell types. By brain region spacial comparisons, we found spatial specificity among excitatory neuronal clusters within the same cortical layer.  We identify brain-region-specific transcription factors that may regulate cortical region development of excitatory neurons. These data define the landscape of cell type and spatial heterogeneity in the rostral mouse brain and the underlining regulatory epigenomic basis.

overall_design:
Apply snmC-seq2 to 118 brain functional regions to identify epigenomic landcape of the adult mouse brain
This submission consists of brain region (MOs).

first: Hanqing

last: Liu

first: Chongyuan

last: Luo

last: Rivkin


title: Fatty liver disease caused by high alcohol-producing Klebsiella pneumoniae

status: Public on Aug 10 2020

first: Jing

last: Lu

address: Beijing, Fengtai District,100071, China

institute: Academy of Military Medical Sciences

summary: To further explore the overall development and progression of hepatic steatosis induced by HiAlc Kpn, we examined liver transcriptional profiles derived HiAlc Kpn-fed, pair-fed, or ethanol-fed mice for the 4th, 6th and 8th week post gavage. The liver gene expressions in mice both with HiAlc Kpn-fed and ethanol-fed have been showed large diversities to pair-fed mice. These results clearly illustrated a process of chronic liver injury, which is consistent with previous “two-hits” insulin hypothesis, and suggested that endogenous ethanol produced by HiAlc Kpn play important roles in the steatohepatitis, as well as alcohol intake.

overall_design: Kpn-fed, pair-fed (negative control), or ethanol-fed induced gene expression in mice was measured at 4th, 6th and 8th week post gavage.

last: Yuan

first: Weiwei

last: Cheng


title: Epigenomic Landscape of Mouse Brain by Single Nucleus Methylation Sequencing [CEMBA171206_3C]

first: Angeline

first: Anna

last: Bartlett

first: Jacinta

last: Lucero

last: Nery

first: Andrew

last: Aldridge

first: Rosa

last: Castanon


title: m6A methylation regulates the fate of endogenous retrovirus transcripts [CUT & RUN]

status: Public on Aug 11 2020

city: paris

first: teissandier

last: aurelie

address: 26 rue d'Ulm

country: France

institute: institut curie

summary: Using a genome-scale CRISPR knockout screening in mouse embryonic stem cells, we identify m6A RNA methylation as an important regulatory component that restricts the activity of endogenous retroviruses of the IAP (intracisternal A-particles) family. The m6A methylation of IAP mRNAs occurs on their 5’ end, is catalyzed by the complex of methyltransferase-like (METTL)3/METTL14 proteins whose depletion, along with other complex subunits, namely WTAP and ZC3H13, leads to increased IAP transcript abundance. Using auxin-dependent degron, we show that rapid removal of METTL3, METTL14 and ZC3H13 further increases IAP RNA abundance in a progressive and reversible fashion. Finally, we demonstrate that m6A RNA reduces the stability of IAP transcripts

overall_design: Genome-wide loss-off-function CRISPR/Cas9 knock out screen using mouse embryonic stem cells carrying IAPEz transposon reporter cassette.

first: Tomasz

last: Chelmicki

first: Aurelie

last: Teissandier


title: Multiregional Glioma Single-Cell Transcriptomic Sequencing

status: Public on Jul 22 2020

first: Kai

last: Yu

address: Yiheyuan Rd. 5th

institute: Peking University

summary: Glioma is a complex malignant neoplasm, treating each case as a dark box obviously could not acquire expected overall prognosis, because subpopulation inside tumor could be core factor which directly influence tumor progression. So, clonal sequencing or single-cell sequencing could be best solution to this problem. Here we combined these two strategies and analyzed more than 6000 single-cell transcriptome of 73 surgery points from 13 glioma and 1 brain metastasis patient. After these cells assigned into normal, immune, tumor and several other groups based on differentially expressed genes and specified TCGA 4 classification gene sets, spacial information of sampling points helped us built up cell type constituent of different part inside tumor, and illustrated invasion patterns during tumor growth.

first: Yuqiong

last: Hu

first: Fan

last: Wu

first: Qiufang

last: Guo

first: Zenghui

last: Qian

first: Waner

first: Tao

last: Jiang

first: Fuchou

last: Tang

first: Xiaodong

last: Su


title: Epigenomic Landscape of Mouse Brain by Single Nucleus Methylation Sequencing [CEMBA180104_4B]

city: La Jolla

first: Joseph

last: Ecker

first: Hanqing

last: Liu

first: Chongyuan

last: Luo

first: Angeline

last: Rivkin

first: Yupeng

last: He

first: Huaming

last: Chen

first: Zhuzhu

last: Zhang

first: Jingtian

last: Zhou

first: Bing

last: Ren

first: Eran

last: Mukamel

first: M

last: Behrens


title: Epigenomic Landscape of Mouse Brain by Single Nucleus Methylation Sequencing [CEMBA171213_4B]

first: Anna

last: Bartlett

first: Jacinta

last: Lucero

last: Nery

first: Andrew

last: Aldridge

first: Rosa

last: Castanon


title: Comparative transcriptome analysis of Solenopsis japonica (Hymenoptera: Formicidae) under low temperature and normal room temperature

status: Public on Aug 01 2020

city: Gimcheon

first: Mohammad

last: Vatanparast

address: 167, Yongjeon-ro

department: Plant quarantine technology center

institute: Animal and Plant Quarantine Agency

summary:
Purpose: We aimed to provide a basis for the adaptive mechanism and a rich resource for the discovery and identification of novel genes involved in the cold stress response in Solenopsis japonica. Retinal transcriptome profiling (RNA-seq) to microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis
Methods: Solenopsis japonica was reared at lab condition, and incubated at 2 different temperature for 24h (9, and 25℃) under dark conditions. RNA was extracted using Trizol reagent and Illumina sequencing was performed at Macrogen. Illumina short reads were quality-filtered and Illumina-based de novo transcriptome assembly was performed. Differential Gene Expression Analysis was studied for different tempearture conditions.
Results: Totally 89,657 unigenes was obtained which overall 43,375 were annotated with gene descriptions, gene ontology terms, and metabolic pathways. 86 GO functional sub-groups and 25 EggNOG terms resulted. DEGs with FC≥2 and FC≤-2, P-value<0.05 were screened and were compared at two different temperatures. We found 138 DEG down regulated and 271 DEG up regulated when the S. japonica incubated at 9 ℃ and compared with 25℃ treated group. Comparing transcriptome profiles for differential gene expression resulted various DE proteins and genes, including cytochrome P450, NADH dehydrogenase subunit 1, cuticle protein and HSP which have previously been reported to be involved in cold and high temperature resistance. GO analysis revealed that antioxidant activity up-regulated under high temperature stress.
Conclusions: we compared the transcriptomes of S. japonica under normal room temperature and low-temperature using RNA-Seq technology based on the high-throughput sequencing. Comparative transcriptome analysis identified many genes and a large number of changes were discovered in metabolic pathway through the GO and KEGG enrichment analysis. Our data will facilitate further molecular investigations and genomic research. Many low-temperature significantly up-regulated genes were first identified in this study. These newly found genes may be important and necessary to S. japonica overwintering and its behavior for adaptation in new environment.

overall_design: Total RNA of Solenopsis japonica for two different treated temperature that 25℃ was used as control.

first: Youngjin

last: Park


title: Fingerstick Blood-Test for Rapid Estimation of Absorbed Radiation Dose

status: Public on Jul 15 2020

city: Columbus

first: NADUPARAMBIL

middle: Korah

last: JACOB

state: Ohio

address: 410 W 12th Ave

department: Radiation Oncology

institute: The Ohio State University

summary: We developed scalable radiation dosimeter based on non-coding miR-150 (radiation sensitive) normalized to endogenous miR-23a (radiation insensitive). This nanoString assay revealed the expression of miR-150 and miR-23a in normal healthy volunteers serum blood cell subsets.

overall_design: Healthy leukopaks were used to pull down specific blood cell subsets such as T-cells, B-cells, NK cells, HSCs and platelets using immunobead antibodies (CD3, CD19, CD56, CD34 and CD61 respectively). Whole blood (WBCs), serum and RBCs were also used to comapre miR-150 and miR-23a percentage of overlap and investigate the percentage of contribution of these miRNAs by blood subsets to the circulation. 100 ng of total miRNA was used in case of blood cell subsets whereas 5 ng of total miRNA was used in case of WBCs and RBCs (due to abundance of miR-451 which intereferes with other miRNA counts) for nanoString assay. nanoString data is from three different leukopak isolation. Raw data from the nanoString assay were technically normalized followed by top 100 miRNA normalization strategy.

first: Sagar

last: Bhayana

first: Marshleen

last: Yadav

first: Xiaokui

last: Mo

first: Paolo

last: Fadda

first: Naduparambil

middle: K

last: Jacob


title: circRNAs in the mouse striatum of HuD KO and wildtype mice

status: Public on Jun 27 2020

city: Albuquerque

first: Nora

last: Perrone-Bizzozero

state: NM

address: 1 University of New Mexico MSC08 4740

department: Neurosciences

institute: University of New Mexico

summary: This study explores how HuD regulates the expression circRNAs in the striatum

overall_design: 3 HuD KO mice vs. 3 WT littermates

first: Rob

last: Oliver

first: Michela

last: Dell'Orco


title: Growth Optimized Aminoacyl-tRNA Synthetase Levels Prevent Maximal tRNA Charging

status: Public on Jul 20 2020

city: Cambridge

first: Darren

middle: John

last: Parker

state: MA

address: 31 Ames Street

department: Biology

institute: MIT

summary:
Summary
Aminoacyl-tRNA synthetases (aaRSs) serve a dual role in charging tRNAs. Their enzymatic activities both provide protein synthesis flux and reduce uncharged tRNA levels. Although uncharged tRNAs can negatively impact bacterial growth, substantial concentrations of tRNAs remain deacylated even under nutrient-rich conditions. Here we show that tRNA charging in Bacillus subtilis is not maximized due to optimization of aaRS production during rapid growth, which prioritizes demands in protein synthesis over charging levels. The presence of uncharged tRNAs is alleviated by precisely tuned translation kinetics and the stringent response, both insensitive to aaRS overproduction but sharply responsive to underproduction, allowing for just-enough aaRS production atop a “fitness cliff”. Notably, we find that the stringent response mitigates fitness defects at all aaRS underproduction levels even without external starvation. Thus, adherence to minimal, flux-satisfying protein production drives limited tRNA charging and provides a basis for the sensitivity and setpoints of an integrated growth-control network.

overall_design: Ribosome profiling and RNA-seq experiments of Bacillus subtilis strains

middle: J

first: Jean-Benoit

last: Lalanne

first: Satoshi

last: Kimura

first: Grace

last: Johnson

first: Matthew

last: Waldor

first: Gene-Wei

last: Li


title: Molecular mechanisms in lung tissue of yak provide insights into high-altitude adaptation by transcriptome-wide analysis [RNA-seq]

status: Public on Jul 08 2020

city: Lanzhou

first: Qianyun

last: Ge

state: Gansu

address: NO.1 yingmen village, Anning district

institute: Gansu Agricultural University

summary:
Purpose：Yak long-term colonization and widespread distribution across the plateau can be serve as an ideal natural animal model to provide insights into the adaptive evolution of other plateau species, including humans.
Methods:To exploring the molecular mechanisms of lung tissue in yak to response to hypoxia, the mRNA, lncRNA and miRNA of lung tissue from cattle and three different altitude yaks were sequenced.
Results:A total of 21764 mRNAs, 14168 lncRNAs and 1209miRNAs (305 known and 904 novel miRNAs)were identifed.Compared yak with cattle, 4975 mRNAs, 3326 lncRNAs and 75 miRNAs were differentially expressed. 756 mRNAs, 346 lncRNAs and 83 miRNAs were found to be differentially expressed amongthree different altitude yaks(fold change≥2 and P-value<0.05).
Conclusions:The differentially expressed genes were functionally enriched in long-chain fatty acid metabolic process and protein processing between yak and cattle, while the immune response and cell cycle were enriched among three different altitude yaks. Furthermore, the competing endogenous RNAs (ceRNAs) networks were identified to illustrate their roles.

sample_organism:
Bos taurus
Bos grunniens

platform_organism:
Bos taurus
Bos grunniens

overall_design: Lung tissues of yak and cattle to identify induced lncRNAs, miRNA and mRNA.

first: Shengguo

last: Zhao


title: Transcriptomic and Chromatin accessibility profiling of functional brown adipocytes derived from human pluripotent stem cells

city: Athens

first: Liang

last: Zhang

state: GA

address: 325 Riverbend Road

department: Biochemistry and Molecular Biology, Center for Molecular Medicine

institute: University of Georgia

summary:
Brown adipocytes (BAs) are a potential therapeutic cell source for the treatment of metabolic disease such as type 2 diabetes. In this report, human pluripotent stem cells (hPSCs) are subject to directed differentiation to brown dipocytes through a paraxial mesoderm intermediate at high-efficiency.
RNA-Seq and ATAC-seq was performed to characterized hPSCs derived paraxial mesoderm and brown adipocytes generated in this study.

overall_design:
RNA-Seq was perfomed on iPSC and hESC derived paraxial mesoderm, iPSC and hESC derived full differentiated brown adipocytes. The differentiation process of  brown adipocytes was also interrogated by RNA-Seq profiling at various differentiation time points.
Time-course ATAC-Seq profiling was perfomed to interrogate the early differentiation process from paraxial mesoderm to brown adipocytes at early differentiation stages.

first: Stephen

last: Dalton


title: RNA-Seq of Human iPSC-cardiomyocytes infected with SARS-CoV-2

status: Public on Jun 19 2020

first: AGCT

last: Core

state: CA

address: 8687 Melrose Ave, PDC B230

institute: Cedars Sinai Medical Center

summary: Coronavirus disease 2019 (COVID-19) is a viral pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). COVID-19 is predominantly defined by respiratory symptoms, but cardiac complications including arrhythmias, heart failure, and viral myocarditis are also prevalent. Although the systemic ischemic and inflammatory responses caused by COVID-19 can detrimentally affect cardiac function, the direct impact of SARS-CoV-2 infection on human cardiomyocytes is not well understood.

overall_design: We used human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) as a model system to examine the mechanisms of cardiomyocyte-specific infection by SARS-CoV-2. These studies show that SARS-CoV-2 can infect hiPSC-CMs in vitro, establishing a model for elucidating the mechanisms of infection and potentially a cardiac-specific antiviral drug screening platform.

first: Arun

last: Sharma

first: Clive

last: Svendsen


title: Molecular mechanisms in lung tissue of yak provide insights into high-altitude adaptation by transcriptome-wide analysis

type: Non-coding RNA profiling by high throughput sequencing

summary: This SuperSeries is composed of the SubSeries listed below.


title: Molecular mechanisms in lung tissue of yak provide insights into high-altitude adaptation by transcriptome-wide analysis [miRNA-seq]


title: Salmonella Typhimurium evades macrophage defense by derailing metabolic pathways

city: Cologne

first: Nirmal

last: Robinson

state: NRW

address: Joseph-Stelzmann-Str. 26

department: Institut für Medizinische Mikrobiologie, Immunologie und Hygiene

institute: CECAD Forschungszentrum

summary: In this study, we have employed RNA seq analysis to comprehensively understand the genes regulated in macrophages upon S.Typhimurium infection. Our data reveal that S. Typhimurium abrogates key metabolic pathways and their modulators. Disruption in metabolism leads to reduced acidification of phagosomes resulting in impaired bacterial clearance and antigen presentation.

overall_design: mRNA profile of bone marrow derived macrophages infected with S.Typhimurium for 2h

first: Saray

last: Gutierrez


title: The serotonin transporter is a regulator of neurodegeneration and axon regeneration after retinal injury

status: Public on Jul 11 2020

city: Pittsburgh

first: Takaaki

last: Kuwajima

address: 1622 Locus Street, 7.396

department: Ophthalmology

institute: University of Pittsburgh School of Medicine

summary: Loss of specialized neurons in neurodegenerative diseases and after nerve injury is mediated in a neuronal subtype- and region-specific fashion. However, little is known about what molecular contexts define selective vulnerability. Here, we demonstrate that retinal ganglion cells (RGCs) in the mouse peripheral ventrotemporal (VT) retina are the most susceptible to optic nerve injury. Mechanistically, we show that the ventral-specific molecule, the serotonin transporter (SERT) is upregulated on VT axons within one day after injury and loss of SERT attenuates VT RGC death and promotes axon regeneration. From RNA-seq analysis, the transmembrane protein Gpnmb has been identified as a target downregulated by SERT. Moreover, GPNMB is involved in RGC protection and axon regeneration. Together, our studies reveal the serotonin transporter as a determinant of selective vulnerability.

overall_design: We performed optic nerve crush (ONC) in wildtype mice and Slc6a4-/- mutants and dissected out the ventrotemporal (VT) region of the injured retina one day after ONC. Total RNA was extraced and transcript levels were analyzed between injured WT and Slc6a4-/- VT retinas. Samples were collected in triplicates and RNA sequencing identified several genes upregulated and downregulated in Slc6a4-/- mutants leading to early SERT-mediated degeneration of RGC and impariment of axon regeneration.

first: Rody

last: Kingston

first: Dwarkesh

last: Amin

first: Sneha

last: Misra

first: Jeffrey

last: Gross


title: ChIP-seq profiling of myogenin and p300 occupancy in the context of rexinoid signaling during early myogenic differentiation

status: Public on Jun 24 2020

city: Ottawa

first: Qiao

state: Ontario

address: 451 smyth road

department: Cellular and Molecular Medicine

country: Canada

institute: University of Ottawa

summary: Deciphering the molecular mechanisms underpinning myoblast differentiation is a critical step in developing the best strategy to promote muscle regeneration in patients suffering from muscle-related diseases. We have previously established that a rexinoid x receptor (RXR)-selective agonist enhances the differentiation and fusion of myoblasts through a direct regulation of MyoD expression, coupled with an augmentation of myogenin protein. Here, we found that RXR signaling modifies the chromatin state distribution of myogenin, promoting the binding preference of myogenin for poised enhancers and a distinct motif. We also found an association of myogenin with rexinoid-responsive gene expression and identified an epigenetic signature related to histone acetyltransferase p300. Moreover, RXR signaling instigates residue-specific histone acetylation at enhancers co-occupied by p300 and myogenin. Thus, genomic distribution of transcriptional regulators is an important designate for identifying novel targets as well as developing therapeutics that modulate epigenetic landscape in a selective manner to promote muscle regeneration.

overall_design: ChIP-seq of myogenin, histone acetyltransferase p300, and H3K27me3 in C2C12 myoblasts differentiated for 24 hours in the absence or presence of bexarotene. Untreated differentiating myoblasts and input chromatin DNA were used as controls.

first: Saadia

last: Khilji

first: Munerah

last: Hamed


title: Genome-wide chip of PDGF-BB induced mesenchymal stem cell.

status: Public on Jun 17 2020

city: Moscow

first: Mikhail

last: Arbatsky

address: Lomonosovskiy 27 bld 10

country: Russia

institute: MSU IRM

summary: We report the application of single-molecule-based sequencing technology for high-throughput profiling of MSC.

overall_design: Define which cytokines induce the most signficant expression changes, describe the results; perform functional assessment of expression changes.

first: M

first: O

last: Grigorieva

first: A

middle: Y

last: Efimenko


title: mRNAs in HuD KO in the mouse striatum

status: Public on Jun 28 2020

first: Nora

last: Perrone-Bizzozero

type:
Expression profiling by array
Non-coding RNA profiling by array

summary: This study explores how HuD regulates the expression circRNAs vs. mRNAs from the same genes

overall_design: 3 HuD KO mice vs. 3 wildtype littermates (WT)

first: Michela

last: Dell'Orco


title: Estrogen-related Receptor Signaling Coordinately Controls Cardiac Energy Metabolic and Structural Maturation

status: Public on Jun 10 2020

city: Philadelphia

first: Tomoya

last: Sakamoto

address: Smilow Center for Translational Research 11th FL (Room 11-172) 3400 Civic Center Blvd Bldg 421

department: Cardiovascular Institute

institute: University of Pennsylvania

overall_design: Refer to individual Series


title: The long non-coding RNA HOTAIRM1 promotes tumor aggressiveness and radiotherapy resistance in glioblastoma

city: Homburg (Saar)

first: Marc

last: Remke

state: Saarland

address: Kirrberger Straße 100, Gebäude 9

department: Pediatric Translational Oncology Lab

institute: Universitätsklinikum des Saarlandes

summary: Glioblastoma is the most common malignant primary brain tumor. Clinically relevant biomarkers are restricted to isocitrate dehydrogenase (IDH) gene 1 or 2 mutation and O6-methylguanine DNA methyltransferase (MGMT) promoter methylation. Long non-coding RNA (lncRNA) alterations may contribute to glioblastoma pathogenesis and potentially serve as novel biomarkers. The clinical significance of HOXA Transcript Antisense RNA, Myeloid-Specific 1 (HOTAIRM1) was analyzed in multiple glioblastoma gene expression data sets for associations with prognosis and IDH mutation and MGMT promoter methylation status. The role of HOTAIRM1 in glioblastoma biology and radiotherapy resistance was characterized in vitro and in vivo. We identified HOTAIRM1 as a candidate lncRNA whose up-regulation is significantly associated with shorter survival of glioblastoma patients independent from IDH mutation and MGMT promoter methylation. Glioblastoma cell line models uniformly showed reduced cell viability, less invasive growth and diminished colony formation capacity upon HOTAIRM1 down-regulation. Integrated proteogenomic analyses and determination of reactive oxygen species (ROS) levels revealed impaired mitochondrial function and increased ROS levels upon HOTAIRM1 knock-down. HOTAIRM1 knock-down decreased expression of transglutaminase 2 (TGM2) as a candidate protein implicated in mitochondrial function, and knock-down of TGM2 mimicked the phenotype of HOTAIRM1 down-regulation in glioblastoma cells. Moreover, HOTAIRM1 modulates radiosensitivity of glioblastoma cells in vitro and in vivo. Our data support a role for HOTAIRM1 as a driver of biological aggressiveness, radioresistance and poor outcome in glioblastoma. Targeting HOTAIRM1 may be a promising new therapeutic approach.

overall_design: For transient knock-down of HOTAIRM1, T98G, LN-229 or U251 glioblastoma cells were seeded (100,000 cells per well) into 6-well plates the day before knock-down. Specific knock-down of HOTAIRM1 and the corresponding non-target negative controls was achieved by using HOTAIRM1-specific siPOOLs (#100506311, siTOOLs Technology, Planegg, Martinsried, Germany), siTOOLs Technology) and non-target siPOOLs (Neg. control siPOOL 5 nmol, siPOOL Technology), respectively. Transfection of siPOOLs was performed using Lipofectamine RNAiMAX Transfection Reagent (#13778150, Thermo Fischer Scientific). Briefly, 7.5 μl RNAiMAX Transfection Reagent was diluted in 125 μl Opti-MEM (#31985062, Thermo Fischer Scientific) pipetted into a well with 0.5 μl (5 pM) siPOOL in 125 μl Opti-MEM. Cells were harvested 72 hours post transfection.

first: Daniel

last: Picard

first: Ulvi

last: Ahmadov


title: Expression data from brain parts (amygdala, hippocampus, prefrontal cortex, and cerebral cortex) from mice with or without chronic mild stress (CMS) treatments.

status: Public on Jun 05 2020

city: Taipei

first: Kang-Yi

last: Su

address: No.1, Jen-Ai Road

department: Department of Clinical Laboratory Sciences and Medical Biotechnology

country: Taiwan

institute: National Taiwan University

summary:
Accumulation of negative stressful life events caused major depressive disorder (MDD) a major public health problem related to disability around the world. For effective therapy and disease managements, a comprehensive genomic analysis to identify objective signatures is required to grasp pathophysiological changes and applicable markers.
This data was from a chronic mild stress (CMS) induced MDD mouse model followed by Affmatrix cDNA expression array (GeneChip Mouse Genome 430 2.0 Array) analysis in amygdala, hippocampus, prefrontal cortex, and cerebral cortex.

overall_design: Mice with or without 4 weeks chromic unpredicted mild stress treatments were sacrificed and total RNAs were extracted from brain parts including amygdala, hippocampus, prefrontal cortex, and cerebral cortex of each independent mouse (n=3 for CMS treated and n=3 for control mice). GeneChip Mouse Genome 430 2.0 Array (Affymetrix, CA, USA) was used for whole genome expression profiling. The procedures are essentially followed according to the manufacturer’s manual.

first: Sung-Liang

last: Yu


title: Microglia depletion and alcohol: Transcriptome and behavioral

status: Public on Jun 01 2020

city: Austin

first: Anna

last: Warden

state: TX

address: 2500 Speedway

institute: University of Texas at Austin

summary:
Purpose: Alcohol abuse induces changes in microglia morphology and immune function, but whether microglia initiate or simply amplify the harmful effects of alcohol exposure is still a matter of debate. Here we determined microglia function in acute and voluntary drinking behaviors using a colony stimulating factor 1 receptor inhibitor (PLX5622) and 3’UTR biased-sequencing. Therefore, The purpose of this study was to provide insight regarding microglia depletion and voluntary alcohol consumption.
Methods: We performed 3’UTR biased transcriptome sequencing (3’Tag-seq) on total homogenate isolated from the prefrontal cortex (PFC) of C57BL6/J mice following microglia depletion and chronic every-other-day alcohol consumption.
Results: Differential expression analysis and WGCNA network analysis revealed that although many immune genes have been implicated in alcohol abuse, downregulation of microglia genes does not necessitate changes in alcohol intake. Finally, we show that microglia depletion and chronic alcohol result in compensatory upregulation of ethanol-responsive, reactive astrocyte genes, indicating astrocytes may play a critical role in regulation of these alcohol behaviors.
Conclusion:Taken together our behavioral and transcriptional data indicate that microglia are not the primary effector cell responsible for regulation of acute and voluntary alcohol behaviors.  In addition, our data represents a novel resource for groups interested in transcriptional effects of microglia depletion after alcohol consumption.

overall_design: Illumina 3'UTR biased-sequencing of total homogenate from PFC of mice following chronic alcohol consumption and microglia depletion

first: R

last: Dayne Mayfield

last: Adron Harris


title: Transcriptomic analysis of a putative LysR family regulator, a putative Dps, and a cystine importer disrupted mutants in radiation resistant bacterium Deinococcus geothermalis

status: Public on Jun 06 2020

city: Seoul

first: Sung-Jae

last: Lee

address: 26 Kyungheedae-ro, Dongdaemun-gu

department: Department of Biology

institute: Kyung Hee University

summary: Here, we compared gene expression level by RNA-Seq analysis among a wild-type (WT) Deinococcus geothermalis strain, a dgeo_2840 of LysR family member gene (Δdgeo_2840), a putative Dps dgeo_0257 (Δdgeo_0257), and a cystine importer dgeo_1986-1987 gene disrupted strain (Δdgeo_1986-1987). From this transcriptomic data, we detected dgeo_2840, dgeo_0257, and dgeo_1986-1987 controlling genes which were somehow up-regulated and/or down-regulated. In particular, Deinococcus geothermalis has a total of 73 insertion sequences (ISs) in genomes, and some of them are actively transposed to other loci with replicative mode by the oxidative stress of hydrogen peroxide treatment.

overall_design: 4 samples including WT and 3 mutant strains.

first: Kyungsil

last: Choo

first: Sung


title: Single-cell transcriptomic analysis of allergen-specific T cells in allergy and asthma [scRNA-Seq]

city: San Diego

first: Pandurangan

last: Vijayanand

state: California

address: 9420 Athena Circle

department: Vaccine Discovery

institute: La Jolla Institute for Immunology

summary: CD4+ helper T cells (TH) and regulatory T cells (Treg) that respond to common allergens play an important role in driving and dampening airway inflammation in patients with asthma. Until recently, direct, unbiased molecular analysis of allergen-reactive TH and Treg cells has not been possible. To better understand the diversity of these T cell subsets in allergy and asthma, we analyzed the single-cell transcriptome of ~50,000 house dust mite (HDM) allergen-reactive TH cells and Treg cells from asthmatics with HDM allergy and from three control groups: asthmatics without HDM allergy and non-asthmatics with and without HDM allergy. Our analyses show that HDM allergen-reactive TH and Treg cells are highly heterogeneous, and certain subsets are quantitatively and qualitatively different in subjects with HDM-reactive asthma. The number of interleukin (IL)-9 expressing HDM-reactive TH cells is greater in asthmatics compared with non-asthmatics with HDM allergy, and display enhanced pathogenic properties. More HDM-reactive Th and Treg cells expressing the interferon-response signature (THIFNR and TregIFNR) are present in asthmatics without HDM allergy compared with those with HDM allergy. In cells from these subsets (THIFNR and TregIFNR), expression of TNFSF10 was enriched; its product, TRAIL, dampens activation of TH cells. These findings suggest that the THIFNR and TregIFNR subsets may dampen allergic responses, which may help explain why only some people develop TH2 responses to nearly ubiquitous allergens.

overall_design: Bulk and single-cell RNA-seq were performed from pure populations of HDM-reactive memory TH and Treg cells were isolated ex vivo from asthmatics with HDM allergy (n = 6) and from three control groups: asthmatics without HDM allergy (n = 6) and non-asthmatics with (n = 6) and without HDM allergy (n = 6)

first: Grégory

last: Seumois

first: Ciro

last: Ramírez-Suástegui

first: Benjamin

last: Schmiedel

first: Shu

last: Liang

first: Bjoern

last: Peters

first: Alessandro

last: Sette


title: Effects of exercise training on skeletal muscle insulin sensitivity in obesity patients undergoing RYGB surgery: a randomized controlled trial

status: Public on May 19 2020

city: Baton Rouge

first: Wagner

middle: S.

last: Dantas

state: LA

address: 6400 Perkins Road

institute: Pennington Biomedical Research Center

summary: We reported that skeletal muscle insulin sensitivity was restored to a lean phenotype with exercise training in patients undergoing RYGB surgery. For that, the goals of this study is to identify changes in the skeletal muscle transcriptome profiling (RNA-seq) that could explain the insulin sensitivity improvement of RYGB + exercise training group.

overall_design: Women patients with morbid obesity were undergone to RYGB and randomized to exercise training or not. Muscle biopsies were assessed before the RYGB surgery (PRE) and 9-month after RYGB surgery in both groups (RYGB and RYGB + exercise training). At baseline (PRE), muscle samples from lean control women were obtained as well.

first: John

last: Kirwan

first: Sujoy

last: Ghosh

first: Richard

last: Carmouche

first: Susan

last: Newman

first: Sara

last: Webb

first: Bruno

last: Gualano


title: The gene expression differences between pancreatic cancer cell lines and its high liver metastatic lines

status: Public on May 01 2020

city: Fukuoka Shi

first: Haimin

last: Feng

address: Maidashi 3-1-1

country: Japan

institute: department of Sugery and Oncology

summary: A significant proportion of differentially expressed genes were associated with extracellular matrix organization and extracellular structure organization.

overall_design: BALB/c AJcl nu/nu female mice were purchased from CLEA (Tokyo, Japan) and transported to our institution at 4-weeks-old. After 1 week, parental PANC-1 and SUIT-2 cells (1×106 cells) were injected into the tail of the pancreas. The mice were humanely killed at 4–7 weeks after injection. Tiny hepatic metastases were harvested and minced. We performed primary culture using minced tissue with collagenase, and the cell culture was then injected into the pancreas. This process was repeated five times to establish the highly metastatic PANC-1 and SUIT-2 cell line.

first: Kenoki

last: Ohuchida

first: Daiki

last: Eguchi

first: Biao

last: Zheng


title: Transcriptomic expression patterns of two contrasting lowland rice varieties reveal high iron stress tolerance

status: Public on May 09 2020

city: Dusseldorf

first: Hans-Joerg

last: Mai

address: Universitaetsstrasse 1

department: Institute of Botany

institute: Heinrich Heine University

summary: Iron (Fe) toxicity is a major challenge for plant cultivation in acidic water-logged soil environments, where lowland rice is a major staple food crop. Only few studies addressed the molecular characterization of excess Fe tolerance in rice, and these highlight different mechanisms for Fe tolerance in the studied varieties. Here, we screened 16 lowland rice varieties for excess Fe stress growth responses to identify contrasting lines, Fe-tolerant Lachit and -susceptible Hacha. Hacha and Lachit differed in their physiological and morphological responses to excess Fe, including leaf growth, leaf rolling, reactive oxygen species generation, Fe and metal contents. These responses were mirrored by differential gene expression patterns, obtained through RNA-sequencing, and corresponding GO term enrichment in tolerant versus susceptible lines. From the comparative transcriptomic profiles between Lachit and Hacha in response to excess Fe stress, individual genes of the category metal homeostasis, mainly root-expressed, may contribute to the tolerance of Lachit. 22 out of these 35 metal homeostasis genes are present in selection sweep genomic regions, in breeding signatures and/or differentiated during rice domestication. These findings will serve to design targeted Fe tolerance breeding of rice crops.

overall_design: 9-day old rice plants of two contrasting rice accessions, Hacha and Lachit, were treated with normal (control) or excess iron concentrations (excess Fe) for 2 days. mRNA profiles were generated in triplicate.

first: Petra

last: Bauer

first: Hans-Jörg


title: Defining codon-mediated mRNA decay and No-go decay in zebrafish embryos

status: Public on May 05 2020

city: Saitama

first: Peixun

last: Han

address: Hirosawa Wako

institute: Riken

summary: The control of mRNA stability plays a central role in regulating gene expression patterns. While much is known about the roles of 5´ and 3´ untranslated regions in the mRNA stability control, the impact of protein-coding sequences on mRNA stability had been obscure. Recently, several groups reported that codon composition in the ORF affects mRNA deadenylation and degradation rates in a translation-dependent manner. Hence, codons define not only the amino acid sequences to be synthesized but also the stability of mRNAs. However, how 61 codons differently affect mRNA stability remains unclear. Besides, aberrant stalling of the ribosome induces ribosome quality control (RQC) and No-go decay. The relationship between the two co-translational mRNA decay pathways is not systematically analyzed.     To precisely characterize the effects of 61 codons on mRNA stability, we developed a simplified reporter system that allows detection of the effect of every single codon on mRNA stability in zebrafish embryos. Using this system, we show that the effect of codons on mRNA stability is partially but significantly correlated with the translation elongation rate and tRNA abundance. Interestingly, the codon effect is still maintained in zebrafish embryos lacking Znf598, an essential mediator of RQC and NGD. Znf598-dependent NGD targets a particular type of ribosome stalling but has limited impact on endogenous mRNA stability. Our study thus defines two related co-translational mRNA decay pathways during animal development.

overall_design: Ribosome profiling

first: Mari

last: Mito

first: Shintaro

last: Iwasaki

first: Yuichiro

last: Mishima